Departments of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.
Biophys J. 2010 Oct 20;99(8):2568-76. doi: 10.1016/j.bpj.2010.08.027.
Actin-related protein 2 and 3 (Arp2/3) complex forms a dendritic network of actin filaments during endocytosis and cellular locomotion by nucleating branches on the sides of preexisting actin filaments. Reconstructions of electron tomograms of branch junctions show how Arp2/3 complex anchors the branch, with Arp2 and Arp3 serving as the first two subunits of the branch. Our aim was to characterize the massive conformational change that moves Arp2 ∼30 Å from its position in crystal structures of inactive Arp2/3 complex to its position in branch junctions. Starting with the inactive crystal structure, we used atomistic-scale molecular dynamics simulations to drive Arp2 toward the position observed in branch junctions. When we applied forces to Arp2 while restraining Arp3, one block of structure (Arp2, subunit ARPC1, the globular domain of ARPC4 and ARPC5) rotated counterclockwise by 30° around a pivot point in an α-helix of ARPC4 (Glu⁸¹-Asn¹⁰⁰) to align Arp2 next to Arp3 in a second block of structure including ARPC3 and the globular domains of ARPC2. This active structure buried more surface area than the inactive conformation. The complex was stable in all simulations. In most simulations, collisions of subdomain 2 of Arp2 with Arp3 impeded the movement of Arp2.
肌动蛋白相关蛋白 2 和 3（Arp2/3）复合物在胞吞作用和细胞运动期间通过在预先存在的肌动蛋白丝的侧面上引发分支来形成肌动蛋白丝的树突状网络。分支结的电子断层重建显示了 Arp2/3 复合物如何固定分支，其中 Arp2 和 Arp3 作为分支的前两个亚基。我们的目的是表征将 Arp2 从无活性 Arp2/3 复合物的晶体结构中的位置移动约 30 Å 的大规模构象变化，使其到达分支结的位置。从无活性的晶体结构开始，我们使用原子尺度的分子动力学模拟将 Arp2 驱动到在分支结中观察到的位置。当我们对 Arp2 施加力同时约束 Arp3 时，一个结构块（Arp2、亚基 ARPC1、ARPC4 和 ARPC5 的球状结构域）围绕 ARPC4（Glu⁸¹-Asn¹⁰⁰）的α螺旋中的一个枢轴点逆时针旋转 30°，使 Arp2 与结构块中的 Arp3 对齐，该结构块包括 ARPC3 和 ARPC2 的球状结构域。这种活性结构比无活性构象埋藏更多的表面积。复合物在所有模拟中都很稳定。在大多数模拟中，Arp2 的亚结构域 2 与 Arp3 的碰撞阻碍了 Arp2 的运动。
